A high resolution model mesh was required to numerically simulate sediment transport in tidal marshes. The timing of flooding is dependent on the tidal marsh ground elevation, which requires accurate topographic elevation data. The tidal prism of the marsh is determined by the volume provided by tidal channels in the system. Hence, their location and bathymetry needed to be represented adequately. Due to the high spatial variability and inaccessibility of marshes, remote sensing techniques such as light detection and ranging (LiDAR) are a significant resource for elevation data. LiDAR measures the highest elevation of elements. To determine the bare ground elevation, filter techniques exist but are often inadequate to eliminate elevation errors that are introduced by the vegetation of marshes. We introduce a simple method to remove remaining vertical elevation errors in high resolution digital terrain models (DTMs) of vegetated marshes and present an approach to determine the bathymetry of tidal channels based on a limited number of cross-sectional measurements. Forcing polygons for mesh generation were extracted from the DTMs to assure an accurate spatial representation of the marsh. DTMs (2 × 2 m/1 × 1 m) derived from LiDAR data from the Blackbird Creek Reserve and Bombay Hook National Wildlife Refuge in Delaware, USA, were used.